e45fcb66eb
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 15:56:19 -04:00
1e6794c539
fixing typo in VariantsToTable docs
2011-10-17 15:56:02 -04:00
0de8550f17
Merged bug fix from Stable into Unstable
2011-10-17 15:29:53 -04:00
c1329c4dde
Fixing a binary to logical or
2011-10-17 15:29:45 -04:00
9e4963efc8
Merged bug fix from Stable into Unstable
2011-10-17 15:27:38 -04:00
ec911ce5bb
Even better error messages
2011-10-17 15:27:22 -04:00
d065bf1715
Merged bug fix from Stable into Unstable
2011-10-17 15:25:47 -04:00
a7cf9cdc67
Fixing error message typo
2011-10-17 15:25:35 -04:00
589df6b7cf
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-17 14:35:14 -04:00
6b02354d84
Adding a new getter in VariantsToTable to extract the indel event length.
2011-10-17 14:34:52 -04:00
3550798c4c
Merged bug fix from Stable into Unstable
2011-10-17 13:58:56 -04:00
4108a294f7
Better error message when a RodBinding file doesn't exist
2011-10-17 13:58:46 -04:00
cc76826f78
Merged bug fix from Stable into Unstable
2011-10-17 13:38:11 -04:00
fd4540cd32
Fixed extraordinarily subtle race condition with contracts invariant
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-- all of the methods in the class must be synchronized or the internal state can be inconsistent with the contract invariant when entering the class in a non-synchronized method, even when that method doesn't care about the object's internal state
2011-10-17 13:37:55 -04:00
5a881360df
Merged bug fix from Stable into Unstable
2011-10-13 15:54:43 -04:00
7cab6f6bb0
Bug fixes for thread unsafe simple timer and bad Ns treatment in AlignmentUtils
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-- SimpleTimer is now threadsafe using synchronized method keywords
-- Bug fix for alignmentToByteArray() where the N case was refPos++ not the now correct refPos += elementLength
2011-10-13 15:53:12 -04:00
9aecd50473
Adding ability to exclude annotations from the VA and UG lists. As described in the docs, this argument trumps all others (including -all) so that we can get around the SnpEff issue brought up by Menachem. Added integration test for it.
2011-10-12 15:44:54 -04:00
e53a952aeb
Added ION Torrent support to CountCovariates.
2011-10-12 01:57:02 -04:00
a2733a451f
Added NotCalled feature to GAV
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Added "not called" and "no status" to the truth table. Very useful.
2011-10-11 19:31:45 -04:00
ae83420637
Merged bug fix from Stable into Unstable
2011-10-11 12:26:08 -04:00
794f275871
SnpEff is now marked as a RodRequiringAnnotation instead of an ExperimentalAnnotation.
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Having SnpEff grouped with the Experimental annotations was proving problematic, since it
requires a rod. Placing it in its own group should improve the situation somewhat, making it
easier to request "all annotations except for SnpEff".
2011-10-11 12:08:56 -04:00
cfd0ac8410
Merged bug fix from Stable into Unstable
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Conflicts:
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
2011-10-11 12:03:51 -04:00
24b72334b3
UnifiedGenotyper now correctly initializes the VariantAnnotator engine.
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This allows the annotation classes to perform any necessary initialization/validation.
For example, it allows the SnpEff annotator to (among other things) validate its rod binding.
This will prevent a NullPointerException when SnpEff annotation is requested but no rod binding
is present.
Added an integration test to cover this case so that it doesn't break again.
2011-10-11 12:02:05 -04:00
0429b38021
Merged bug fix from Stable into Unstable
2011-10-11 11:19:38 -04:00
1c485d8b5e
Forgot that no matter how trivial a change it's a good idea to compile first
2011-10-11 11:18:41 -04:00
6418f4d69b
Merged bug fix from Stable into Unstable
2011-10-11 11:13:18 -04:00
1975de1b32
Second try: hide --do_indel_quality in AnalyzeCovariates
2011-10-11 11:11:29 -04:00
6506ea83e8
Revert "Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users"... a hidden passenger change made it through.
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This reverts commit 70e10ccb1be90dcff8f4485ae6ee036db2d1ac86.
2011-10-11 11:03:12 -04:00
4c1d8c8d44
Hide --do_indel_quality argument in AnalyzeCovariates. This shouldn't be documented nor used by external users
2011-10-11 11:01:06 -04:00
77c983c5b5
No one claimed this walker and it doesn't have integration tests or GATKdocs so it doesn't belong in public.
2011-10-10 15:17:54 -04:00
fb72bcf732
DiffObjects no longer prints out the file name in the status so MD5 are stable
2011-10-10 15:10:57 -04:00
46e7370128
this.allele, getAlleles(), and getAltAlleles() now return List not set
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-- Changes associated code throughout the codebase
-- Updated necessary (but minimal) UnitTests to reflect new behavior
-- Much better makealleles() function in VC.java that enforces a lot of key constraints in VC
2011-10-09 11:45:55 -07:00
c67f6c076b
simpleMerge now preserves allele order
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-- UnitTests for dangerous PL merging cases in the multi-allelic case. The new behavior is correct
2011-10-08 17:39:53 -07:00
ec14a4a606
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-07 08:38:50 -07:00
ca9cd9b688
Minor fix for merging intervals which hadn't been necessary when only merging from the left to right. Added integration tests to cover the parallelization of RTC.
2011-10-06 22:38:44 -04:00
c7864c7256
Filter application order is now deterministic, in the order defined by the walker
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-- For no apparent reason we were using a HashSet to store the ReadFilters, so the order of operations was really arbitrarily applied. The order now is
(1) the order of the walker intrinsic filters
(2) read group black list (if provided)
(3) command line filters (if provided)
2011-10-06 18:51:40 -07:00
0b88af4af9
Counts of records failing filters are displayed sorted
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-- Stops random ordering of the output, as the counts are returned sorted by string name of the class
-- Deleted now unused sh*tty assessors in Utils
2011-10-06 18:42:26 -07:00
d1e70d6ec2
Removed Nx counting of reads in metrics with -nt > 1
2011-10-06 18:29:26 -07:00
c61804a450
Rename the long version of the argument name to more accurately reflect its purpose.
2011-10-06 16:14:04 -04:00
61a3dfae24
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 15:58:04 -04:00
6eb87bf58a
RTC now caches all intervals as GenomeLocs (which is expected to take < 1Gb whole genome based on back of the envelope calculations with Matt) so that 1) we don't have to worry about emitting outside of the leaves in the hierarchical reductions and 2) we can emit the intervals in sorted order which is a big performance plus for the realigner. Integration tests change only because intervals whose start=stop are now printed as chr:start instead of chr:start-stop.
2011-10-06 15:57:49 -04:00
1b0735f0a3
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 13:41:45 -04:00
c4dfc1fb8b
Temporary commit of parallelization support for RealignerTargetCreator. Tim begged us for this and I got assurances from Khalid/Matt that this would also be extremely helpful for the whole genome calling pipeline, so I spent a while working on this. Needs to be fixed up though because apparently only the leaves in the hierarchical reduce get their output aggregated. Worked out a better solution with Matt.
2011-10-06 13:41:36 -04:00
73f9d1f217
GATK read group requirement iron hand
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-- The GATK will now throw a user exception if it opens a SAM/BAM file that doesn't have at least one RG defined
-- LIBS again throws an error if the complete list of samples isn't provided
-- Updating ExmpleCountLociPipeline test to use the well-formated versions of the exampleBAM and exampleFASTA files in testdata, instead of the old broken ones in validation_data.
-- Convenience constructors for UserExceptions.MalformedBAM
2011-10-06 08:40:35 -07:00
23845ac798
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 08:17:08 -07:00
daa5999489
Fixed typo in argument description
2011-10-06 08:16:25 -07:00
8a474e38ff
Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-06 10:08:39 -04:00
93f7e632bd
Minor fix/enhancement for VariantEval: if a vcf has symbolic alleles, program would crash ungracefully - now we'll just skip record without processing. This is a big issue since we can't process 1000G integration files with code as is.
2011-10-06 10:07:46 -04:00
190be4d0d1
Merge branch 'master' of ssh://gsa1/humgen/gsa-scr1/gsa-engineering/git/unstable
2011-10-05 21:27:11 -07:00
8e6845806a
Allowing empty samples list in LIBS
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-- Right now we cannot process BAM files without read groups because we enforce the samples list to not be empty when there's a SAM record. Now if there are reads and there are no samples we add the "null" sample so that LIBS walks the reads properly
2011-10-05 21:26:21 -07:00
Ryan Poplin
Mark DePristo
Eric Banks
Mauricio Carneiro
David Roazen
Guillermo del Angel